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#define _FILE_OFFSET_BITS 64 |
2 |
|
3 |
#include <string.h> |
4 |
#include <iostream> |
5 |
#include <fstream> |
6 |
#include <algorithm> |
7 |
#include <utility> |
8 |
|
9 |
#ifdef IS_MPI |
10 |
#include <mpi.h> |
11 |
#include "mpiSimulation.hpp" |
12 |
|
13 |
namespace dWrite{ |
14 |
void DieDieDie( void ); |
15 |
} |
16 |
|
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using namespace dWrite; |
18 |
#endif //is_mpi |
19 |
|
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#include "ReadWrite.hpp" |
21 |
#include "simError.h" |
22 |
|
23 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
24 |
|
25 |
entry_plug = the_entry_plug; |
26 |
|
27 |
#ifdef IS_MPI |
28 |
if(worldRank == 0 ){ |
29 |
#endif // is_mpi |
30 |
|
31 |
|
32 |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
|
34 |
if( !dumpFile ){ |
35 |
|
36 |
sprintf( painCave.errMsg, |
37 |
"Could not open \"%s\" for dump output.\n", |
38 |
entry_plug->sampleName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
43 |
#ifdef IS_MPI |
44 |
} |
45 |
|
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//sort the local atoms by global index |
47 |
sortByGlobalIndex(); |
48 |
|
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for dumping.\n"); |
51 |
MPIcheckPoint(); |
52 |
#endif // is_mpi |
53 |
} |
54 |
|
55 |
DumpWriter::~DumpWriter( ){ |
56 |
|
57 |
#ifdef IS_MPI |
58 |
if(worldRank == 0 ){ |
59 |
#endif // is_mpi |
60 |
|
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dumpFile.close(); |
62 |
|
63 |
#ifdef IS_MPI |
64 |
} |
65 |
#endif // is_mpi |
66 |
} |
67 |
|
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#ifdef IS_MPI |
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|
70 |
/** |
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* A hook function to load balancing |
72 |
*/ |
73 |
|
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void DumpWriter::update(){ |
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sortByGlobalIndex(); |
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} |
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|
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/** |
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* Auxiliary sorting function |
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*/ |
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|
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
83 |
return p1.second < p2.second; |
84 |
} |
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|
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/** |
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* Sorting the local index by global index |
88 |
*/ |
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|
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void DumpWriter::sortByGlobalIndex(){ |
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Atom** atoms = entry_plug->atoms; |
92 |
|
93 |
indexArray.clear(); |
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|
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
96 |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
97 |
|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
99 |
} |
100 |
#endif |
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|
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void DumpWriter::writeDump(double currentTime){ |
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|
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ofstream finalOut; |
105 |
vector<ofstream*> fileStreams; |
106 |
|
107 |
#ifdef IS_MPI |
108 |
if(worldRank == 0 ){ |
109 |
|
110 |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 |
if( !finalOut ){ |
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sprintf( painCave.errMsg, |
113 |
"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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#endif // is_mpi |
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|
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fileStreams.push_back(&finalOut); |
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fileStreams.push_back(&dumpFile); |
123 |
|
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writeFrame(fileStreams, currentTime); |
125 |
|
126 |
#ifdef IS_MPI |
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finalOut.close(); |
128 |
#endif |
129 |
|
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} |
131 |
|
132 |
void DumpWriter::writeFinal(double currentTime){ |
133 |
|
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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
136 |
|
137 |
#ifdef IS_MPI |
138 |
if(worldRank == 0 ){ |
139 |
|
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
141 |
|
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if( !finalOut ){ |
143 |
sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
149 |
|
150 |
} |
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#endif // is_mpi |
152 |
|
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fileStreams.push_back(&finalOut); |
154 |
writeFrame(fileStreams, currentTime); |
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|
156 |
#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
159 |
|
160 |
} |
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|
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void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
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|
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
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|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
169 |
|
170 |
int i, k; |
171 |
|
172 |
#ifdef IS_MPI |
173 |
|
174 |
/********************************************************************* |
175 |
* Documentation? You want DOCUMENTATION? |
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* |
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* Why all the potatoes below? |
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* |
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* To make a long story short, the original version of DumpWriter |
180 |
* worked in the most inefficient way possible. Node 0 would |
181 |
* poke each of the node for an individual atom's formatted data |
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* as node 0 worked its way down the global index. This was particularly |
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* inefficient since the method blocked all processors at every atom |
184 |
* (and did it twice!). |
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* |
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* An intermediate version of DumpWriter could be described from Node |
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* zero's perspective as follows: |
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* |
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* 1) Have 100 of your friends stand in a circle. |
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* 2) When you say go, have all of them start tossing potatoes at |
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* you (one at a time). |
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* 3) Catch the potatoes. |
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* |
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* It was an improvement, but MPI has buffers and caches that could |
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* best be described in this analogy as "potato nets", so there's no |
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* need to block the processors atom-by-atom. |
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* |
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* This new and improved DumpWriter works in an even more efficient |
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* way: |
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* |
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* 1) Have 100 of your friend stand in a circle. |
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* 2) When you say go, have them start tossing 5-pound bags of |
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* potatoes at you. |
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* 3) Once you've caught a friend's bag of potatoes, |
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* toss them a spud to let them know they can toss another bag. |
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* |
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* How's THAT for documentation? |
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* |
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*********************************************************************/ |
210 |
|
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int *potatoes; |
212 |
int myPotato; |
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|
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int nProc; |
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int j, which_node, done, which_atom, local_index, currentIndex; |
216 |
double atomData6[6]; |
217 |
double atomData13[13]; |
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int isDirectional; |
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char* atomTypeString; |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
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|
222 |
#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
224 |
#endif //is_mpi |
225 |
|
226 |
double q[4]; |
227 |
DirectionalAtom* dAtom; |
228 |
Atom** atoms = entry_plug->atoms; |
229 |
double pos[3], vel[3]; |
230 |
|
231 |
#ifndef IS_MPI |
232 |
|
233 |
for(k = 0; k < outFile.size(); k++){ |
234 |
*outFile[k] << nAtoms << "\n"; |
235 |
|
236 |
*outFile[k] << currentTime << ";\t" |
237 |
<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
240 |
|
241 |
<< entry_plug->Hmat[0][1] << "\t" |
242 |
<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
244 |
|
245 |
<< entry_plug->Hmat[0][2] << "\t" |
246 |
<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";"; |
248 |
|
249 |
//write out additional parameters, such as chi and eta |
250 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
251 |
} |
252 |
|
253 |
for( i=0; i<nAtoms; i++ ){ |
254 |
|
255 |
atoms[i]->getPos(pos); |
256 |
atoms[i]->getVel(vel); |
257 |
|
258 |
sprintf( tempBuffer, |
259 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
260 |
atoms[i]->getType(), |
261 |
pos[0], |
262 |
pos[1], |
263 |
pos[2], |
264 |
vel[0], |
265 |
vel[1], |
266 |
vel[2]); |
267 |
strcpy( writeLine, tempBuffer ); |
268 |
|
269 |
if( atoms[i]->isDirectional() ){ |
270 |
|
271 |
dAtom = (DirectionalAtom *)atoms[i]; |
272 |
dAtom->getQ( q ); |
273 |
|
274 |
sprintf( tempBuffer, |
275 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
277 |
q[1], |
278 |
q[2], |
279 |
q[3], |
280 |
dAtom->getJx(), |
281 |
dAtom->getJy(), |
282 |
dAtom->getJz()); |
283 |
strcat( writeLine, tempBuffer ); |
284 |
} |
285 |
else |
286 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
287 |
|
288 |
for(k = 0; k < outFile.size(); k++) |
289 |
*outFile[k] << writeLine; |
290 |
} |
291 |
|
292 |
#else // is_mpi |
293 |
|
294 |
/* code to find maximum tag value */ |
295 |
|
296 |
int *tagub, flag, MAXTAG; |
297 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
298 |
if (flag) { |
299 |
MAXTAG = *tagub; |
300 |
} else { |
301 |
MAXTAG = 32767; |
302 |
} |
303 |
|
304 |
int haveError; |
305 |
|
306 |
MPI_Status istatus; |
307 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
308 |
|
309 |
// write out header and node 0's coordinates |
310 |
|
311 |
if( worldRank == 0 ){ |
312 |
|
313 |
// Node 0 needs a list of the magic potatoes for each processor; |
314 |
|
315 |
nProc = mpiSim->getNumberProcessors(); |
316 |
potatoes = new int[nProc]; |
317 |
|
318 |
//write out the comment lines |
319 |
for (i = 0; i < nProc; i++) |
320 |
potatoes[i] = 0; |
321 |
|
322 |
for(k = 0; k < outFile.size(); k++){ |
323 |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
324 |
|
325 |
*outFile[k] << currentTime << ";\t" |
326 |
<< entry_plug->Hmat[0][0] << "\t" |
327 |
<< entry_plug->Hmat[1][0] << "\t" |
328 |
<< entry_plug->Hmat[2][0] << ";\t" |
329 |
|
330 |
<< entry_plug->Hmat[0][1] << "\t" |
331 |
<< entry_plug->Hmat[1][1] << "\t" |
332 |
<< entry_plug->Hmat[2][1] << ";\t" |
333 |
|
334 |
<< entry_plug->Hmat[0][2] << "\t" |
335 |
<< entry_plug->Hmat[1][2] << "\t" |
336 |
<< entry_plug->Hmat[2][2] << ";"; |
337 |
|
338 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
339 |
} |
340 |
|
341 |
currentIndex = 0; |
342 |
|
343 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
344 |
|
345 |
// Get the Node number which has this atom; |
346 |
|
347 |
which_node = AtomToProcMap[i]; |
348 |
|
349 |
if (which_node != 0) { |
350 |
|
351 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
352 |
// The potato was going to exceed the maximum value, |
353 |
// so wrap this processor potato back to 0: |
354 |
|
355 |
potatoes[which_node] = 0; |
356 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
357 |
|
358 |
} |
359 |
|
360 |
myPotato = potatoes[which_node]; |
361 |
|
362 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
363 |
myPotato, MPI_COMM_WORLD, &istatus); |
364 |
|
365 |
atomTypeString = MPIatomTypeString; |
366 |
|
367 |
myPotato++; |
368 |
|
369 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
370 |
myPotato, MPI_COMM_WORLD, &istatus); |
371 |
|
372 |
myPotato++; |
373 |
|
374 |
if (isDirectional) { |
375 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
376 |
myPotato, MPI_COMM_WORLD, &istatus); |
377 |
} else { |
378 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
379 |
myPotato, MPI_COMM_WORLD, &istatus); |
380 |
} |
381 |
|
382 |
myPotato++; |
383 |
potatoes[which_node] = myPotato; |
384 |
|
385 |
} else { |
386 |
|
387 |
haveError = 0; |
388 |
which_atom = i; |
389 |
|
390 |
local_index = indexArray[currentIndex].first; |
391 |
|
392 |
if (which_atom == indexArray[currentIndex].second) { |
393 |
|
394 |
atomTypeString = atoms[local_index]->getType(); |
395 |
|
396 |
atoms[local_index]->getPos(pos); |
397 |
atoms[local_index]->getVel(vel); |
398 |
|
399 |
atomData6[0] = pos[0]; |
400 |
atomData6[1] = pos[1]; |
401 |
atomData6[2] = pos[2]; |
402 |
|
403 |
atomData6[3] = vel[0]; |
404 |
atomData6[4] = vel[1]; |
405 |
atomData6[5] = vel[2]; |
406 |
|
407 |
isDirectional = 0; |
408 |
|
409 |
if( atoms[local_index]->isDirectional() ){ |
410 |
|
411 |
isDirectional = 1; |
412 |
|
413 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
414 |
dAtom->getQ( q ); |
415 |
|
416 |
for (int j = 0; j < 6 ; j++) |
417 |
atomData13[j] = atomData6[j]; |
418 |
|
419 |
atomData13[6] = q[0]; |
420 |
atomData13[7] = q[1]; |
421 |
atomData13[8] = q[2]; |
422 |
atomData13[9] = q[3]; |
423 |
|
424 |
atomData13[10] = dAtom->getJx(); |
425 |
atomData13[11] = dAtom->getJy(); |
426 |
atomData13[12] = dAtom->getJz(); |
427 |
} |
428 |
|
429 |
} else { |
430 |
sprintf(painCave.errMsg, |
431 |
"Atom %d not found on processor %d\n", |
432 |
i, worldRank ); |
433 |
haveError= 1; |
434 |
simError(); |
435 |
} |
436 |
|
437 |
if(haveError) DieDieDie(); |
438 |
|
439 |
currentIndex ++; |
440 |
} |
441 |
// If we've survived to here, format the line: |
442 |
|
443 |
if (!isDirectional) { |
444 |
|
445 |
sprintf( writeLine, |
446 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
447 |
atomTypeString, |
448 |
atomData6[0], |
449 |
atomData6[1], |
450 |
atomData6[2], |
451 |
atomData6[3], |
452 |
atomData6[4], |
453 |
atomData6[5]); |
454 |
|
455 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
456 |
|
457 |
} else { |
458 |
|
459 |
sprintf( writeLine, |
460 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
461 |
atomTypeString, |
462 |
atomData13[0], |
463 |
atomData13[1], |
464 |
atomData13[2], |
465 |
atomData13[3], |
466 |
atomData13[4], |
467 |
atomData13[5], |
468 |
atomData13[6], |
469 |
atomData13[7], |
470 |
atomData13[8], |
471 |
atomData13[9], |
472 |
atomData13[10], |
473 |
atomData13[11], |
474 |
atomData13[12]); |
475 |
|
476 |
} |
477 |
|
478 |
for(k = 0; k < outFile.size(); k++) |
479 |
*outFile[k] << writeLine; |
480 |
} |
481 |
|
482 |
for(k = 0; k < outFile.size(); k++) |
483 |
outFile[k]->flush(); |
484 |
|
485 |
sprintf( checkPointMsg, |
486 |
"Sucessfully took a dump.\n"); |
487 |
|
488 |
MPIcheckPoint(); |
489 |
|
490 |
delete[] potatoes; |
491 |
|
492 |
} else { |
493 |
|
494 |
// worldRank != 0, so I'm a remote node. |
495 |
|
496 |
// Set my magic potato to 0: |
497 |
|
498 |
myPotato = 0; |
499 |
currentIndex = 0; |
500 |
|
501 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
502 |
|
503 |
// Am I the node which has this atom? |
504 |
|
505 |
if (AtomToProcMap[i] == worldRank) { |
506 |
|
507 |
if (myPotato + 3 >= MAXTAG) { |
508 |
|
509 |
// The potato was going to exceed the maximum value, |
510 |
// so wrap this processor potato back to 0 (and block until |
511 |
// node 0 says we can go: |
512 |
|
513 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
514 |
|
515 |
} |
516 |
which_atom = i; |
517 |
local_index = indexArray[currentIndex].first; |
518 |
|
519 |
if (which_atom == indexArray[currentIndex].second) { |
520 |
|
521 |
atomTypeString = atoms[local_index]->getType(); |
522 |
|
523 |
atoms[local_index]->getPos(pos); |
524 |
atoms[local_index]->getVel(vel); |
525 |
|
526 |
atomData6[0] = pos[0]; |
527 |
atomData6[1] = pos[1]; |
528 |
atomData6[2] = pos[2]; |
529 |
|
530 |
atomData6[3] = vel[0]; |
531 |
atomData6[4] = vel[1]; |
532 |
atomData6[5] = vel[2]; |
533 |
|
534 |
isDirectional = 0; |
535 |
|
536 |
if( atoms[local_index]->isDirectional() ){ |
537 |
|
538 |
isDirectional = 1; |
539 |
|
540 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
541 |
dAtom->getQ( q ); |
542 |
|
543 |
for (int j = 0; j < 6 ; j++) |
544 |
atomData13[j] = atomData6[j]; |
545 |
|
546 |
atomData13[6] = q[0]; |
547 |
atomData13[7] = q[1]; |
548 |
atomData13[8] = q[2]; |
549 |
atomData13[9] = q[3]; |
550 |
|
551 |
atomData13[10] = dAtom->getJx(); |
552 |
atomData13[11] = dAtom->getJy(); |
553 |
atomData13[12] = dAtom->getJz(); |
554 |
} |
555 |
|
556 |
} else { |
557 |
sprintf(painCave.errMsg, |
558 |
"Atom %d not found on processor %d\n", |
559 |
i, worldRank ); |
560 |
haveError= 1; |
561 |
simError(); |
562 |
} |
563 |
|
564 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
565 |
|
566 |
// null terminate the string before sending (just in case): |
567 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
568 |
|
569 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
570 |
myPotato, MPI_COMM_WORLD); |
571 |
|
572 |
myPotato++; |
573 |
|
574 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
575 |
myPotato, MPI_COMM_WORLD); |
576 |
|
577 |
myPotato++; |
578 |
|
579 |
if (isDirectional) { |
580 |
|
581 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
582 |
myPotato, MPI_COMM_WORLD); |
583 |
|
584 |
} else { |
585 |
|
586 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
587 |
myPotato, MPI_COMM_WORLD); |
588 |
} |
589 |
|
590 |
myPotato++; |
591 |
currentIndex++; |
592 |
} |
593 |
} |
594 |
|
595 |
sprintf( checkPointMsg, |
596 |
"Sucessfully took a dump.\n"); |
597 |
MPIcheckPoint(); |
598 |
|
599 |
} |
600 |
|
601 |
#endif // is_mpi |
602 |
} |
603 |
|
604 |
#ifdef IS_MPI |
605 |
|
606 |
// a couple of functions to let us escape the write loop |
607 |
|
608 |
void dWrite::DieDieDie( void ){ |
609 |
|
610 |
MPI_Finalize(); |
611 |
exit (0); |
612 |
} |
613 |
|
614 |
#endif //is_mpi |